It's the same reason we don't let newbies comment either. It just isn't necessary. We let them comment on their own questions and answers but not others because we feel they haven't gotten situated into the StackExchange.
I'm pretty sure that especially when someone is new to SO and doesn't know exactly how the questions should be formalized - and let's be honest how many of us did read the FAQ right after registration...
and ironically I think that just makes the point even clearer. Because these new users don't know what a formal question is and because they probably didn't read the FAQ, they should not have any real reason to flag questions or comments.
I really like Martijn Pieter's answer for this as well in the comments above so I'm including it here:
I fear many a hot-head newbie not yet familiar with the site will flag any comment pointing out a flaw in their question as offensive. How much of a problem is there really? As in, offensive comments on newbie questions that remain unflagged.
From StackExchange's perspective, as I see it, new users should simply focus on asking questions, finding/giving answers, and getting to know the StackExchange culture. There are enough members who can flag already and we don't NEED more people to do it, regardless if they are qualified or not.